# HG changeset patch
# User mingchen0919
# Date 1528817048 14400
# Node ID 9dabaecf12ff900345bf509cdf382c7535adf751
# Parent  a1dfadeb3b59fcfc6f11ff8beaa5841d7e9ebcd1
planemo upload for repository https://github.com/feltus/BDSS

diff -r a1dfadeb3b59 -r 9dabaecf12ff rmarkdown_report.Rmd
--- a/rmarkdown_report.Rmd	Tue Jun 12 11:13:54 2018 -0400
+++ b/rmarkdown_report.Rmd	Tue Jun 12 11:24:08 2018 -0400
@@ -103,9 +103,9 @@
     write(command_stdout, file = paste0(Sys.getenv('REPORT_FILES_PATH'), '/bdss-download.log.txt'), append = TRUE)
     # convert .sra to .fastq/.fasta
     if(opt$X_f == 'fasta') {
-      command = paste0('fastq-dump --fasta --split-files -O ',pe_dir, ' ', id, '.sra')
+      command = paste0('fastq-dump --fasta --split-files -O ', pe_dir, ' ', id, '.sra')
     } else {
-      command = paste0('fastq-dump --split-files -O ',pe_dir, ' ', id, '.sra')
+      command = paste0('fastq-dump --split-files -O ', pe_dir, ' ', id, '.sra')
     }
     cat('----convert SRA to fastq/fasta------\n')
     command_stdout = system(command, intern = TRUE)
@@ -113,7 +113,7 @@
     if(!(paste0(id, '_2.', opt$X_f) %in% list.files('pe_read_files_dir'))) {
       # this is not a paired end SRA file. The corresponding file will be deleted.
       cat(paste0(id, ' is not paired end SRA, the corresponding fastq/fasta file will deleted.'))
-      command_stdout = system(paste0('rm pe_read_files_dir/', id, '_1.*'), intern = TRUE)
+      command_stdout = system(paste0('rm ', pe_dir, ' ', id, '_1.*'), intern = TRUE)
     }
     
 }